For the entire intercalation/deintercalation range of Na4VP2O9, quantum mechanics is applied to investigate sodium transport mechanism and a machine learning force field is used instead of ab initio method to offers an applicable method for the full understanding of the complicated Na + movements dynamically. It shows chain of '8′ shaped units horizontally and repeated alternating round aggregate and '8′ shaped long chain vertically. For primitive Na4VP2O9, facile Na+ transportation along a-axis is observed with an energy barrier of 0.16 V. As a cathode material, Na3VP2O9 also shows fast Na + diffusion with a minimal diffusion energy barrier 0.27 eV along a-axis. However, for the fully sodiated state of Na4VP2O9, Na+ diffusion in the lattice is significantly restricted with an energy barrier of 0.92 eV along b-axis. Accordingly, the sodium ion diffusion coefficients at room temperature for Na3VP2O9, Na4VP2O9 and Na5VP2O9 are 1.2 × 10−9 cm2 s−1, 5.9 × 10−9 cm2 s−1 and 8.2 × 10−11 cm2 s−1, respectively. The formation energy convex hull originated from the removal of Na1 sites and the occupation of E8cO8 cavities reveals an intermediate phase, Na3.5VP2O9, for the NaxVP2O9 (3 ≤ x ≤ 4) and three intermediate phases, Na4.5VP2O9, Na4.625VP2O9 and Na4.75VP2O9, for the NaxVP2O9 (4 ≤ x ≤ 5).